Table II.

General overview of PM/CB nLC-ESI-MS/MS and nLC-MALDI-MS/MS experiments performed

Shown are the number of repetitive runs, search engine enzyme definitions used, mean peptides identified per single nLC run, total identified peptides, identified TM peptides, false discovery rates against decoy database, mean proteins identified per single nLC run, total identified proteins, number of one-hit wonders, one-hit wonders identified solely by one small <700-Da peptide, and decoy database hits of <700-Da peptides. Data from all single run experiments are given in supplemental Table S5. Combined peptide and protein data are given in supplemental Tables S1 and S2.

	Sample
	PM trypsin MALDI	PM elastase MALDI	PM elastase ESI	CB elastase MALDI	CB elastase ESI
No. of runs	4	6	4	4	3
Search specificity	KR	None	None	None	None
Peptides (mean ± S.D.)	145 ± 40	229 ± 49	808 ± 182	521 ± 100	1205 ± 143
Identified peptides	264	673	1675	1443	2786
TM peptides	20	174	604	149	749
False positive (%)	10.6	3.3	13.8	2.1	11.9
Proteins (mean ± S.D.)	98 ± 19	58 ± 13	225 ± 38	155 ± 40	449 ± 57
Identified proteins	160/52	165/56	451/148	339/154	820/358
One-hit wonders	108	109	303	185	462
One-hit wonders <700 Da	0	0	146	0	190
Decoy hits <700 Da (%)	0	0	33.9	0	34.4